Job ID = 10714462 sra ファイルのダウンロード中... Completed: 1576581K bytes transferred in 30 seconds (421442K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 24712379 spots for /home/okishinya/chipatlas/results/ce10/SRX4085378/SRR7167407.sra Written 24712379 spots for /home/okishinya/chipatlas/results/ce10/SRX4085378/SRR7167407.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:54 24712379 reads; of these: 24712379 (100.00%) were paired; of these: 14407246 (58.30%) aligned concordantly 0 times 8774803 (35.51%) aligned concordantly exactly 1 time 1530330 (6.19%) aligned concordantly >1 times ---- 14407246 pairs aligned concordantly 0 times; of these: 704789 (4.89%) aligned discordantly 1 time ---- 13702457 pairs aligned 0 times concordantly or discordantly; of these: 27404914 mates make up the pairs; of these: 18590677 (67.84%) aligned 0 times 7784439 (28.41%) aligned exactly 1 time 1029798 (3.76%) aligned >1 times 62.39% overall alignment rate Time searching: 00:18:54 Overall time: 00:18:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 993114 / 10737144 = 0.0925 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 03 Jun 2018 13:10:22: # Command line: callpeak -t SRX4085378.bam -f BAM -g ce -n SRX4085378.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085378.10 # format = BAM # ChIP-seq file = ['SRX4085378.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:10:22: # Command line: callpeak -t SRX4085378.bam -f BAM -g ce -n SRX4085378.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085378.20 # format = BAM # ChIP-seq file = ['SRX4085378.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:10:22: # Command line: callpeak -t SRX4085378.bam -f BAM -g ce -n SRX4085378.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085378.05 # format = BAM # ChIP-seq file = ['SRX4085378.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:10:22: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:22: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:22: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:22: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:10:22: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:10:22: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:10:30: 1000000 INFO @ Sun, 03 Jun 2018 13:10:30: 1000000 INFO @ Sun, 03 Jun 2018 13:10:30: 1000000 INFO @ Sun, 03 Jun 2018 13:10:37: 2000000 INFO @ Sun, 03 Jun 2018 13:10:37: 2000000 INFO @ Sun, 03 Jun 2018 13:10:37: 2000000 INFO @ Sun, 03 Jun 2018 13:10:45: 3000000 INFO @ Sun, 03 Jun 2018 13:10:45: 3000000 INFO @ Sun, 03 Jun 2018 13:10:45: 3000000 INFO @ Sun, 03 Jun 2018 13:10:52: 4000000 INFO @ Sun, 03 Jun 2018 13:10:52: 4000000 INFO @ Sun, 03 Jun 2018 13:10:52: 4000000 INFO @ Sun, 03 Jun 2018 13:10:59: 5000000 INFO @ Sun, 03 Jun 2018 13:11:00: 5000000 INFO @ Sun, 03 Jun 2018 13:11:00: 5000000 INFO @ Sun, 03 Jun 2018 13:11:07: 6000000 INFO @ Sun, 03 Jun 2018 13:11:07: 6000000 INFO @ Sun, 03 Jun 2018 13:11:07: 6000000 INFO @ Sun, 03 Jun 2018 13:11:14: 7000000 INFO @ Sun, 03 Jun 2018 13:11:15: 7000000 INFO @ Sun, 03 Jun 2018 13:11:15: 7000000 INFO @ Sun, 03 Jun 2018 13:11:21: 8000000 INFO @ Sun, 03 Jun 2018 13:11:23: 8000000 INFO @ Sun, 03 Jun 2018 13:11:23: 8000000 INFO @ Sun, 03 Jun 2018 13:11:28: 9000000 INFO @ Sun, 03 Jun 2018 13:11:30: 9000000 INFO @ Sun, 03 Jun 2018 13:11:30: 9000000 INFO @ Sun, 03 Jun 2018 13:11:35: 10000000 INFO @ Sun, 03 Jun 2018 13:11:38: 10000000 INFO @ Sun, 03 Jun 2018 13:11:38: 10000000 INFO @ Sun, 03 Jun 2018 13:11:43: 11000000 INFO @ Sun, 03 Jun 2018 13:11:45: 11000000 INFO @ Sun, 03 Jun 2018 13:11:45: 11000000 INFO @ Sun, 03 Jun 2018 13:11:51: 12000000 INFO @ Sun, 03 Jun 2018 13:11:53: 12000000 INFO @ Sun, 03 Jun 2018 13:11:53: 12000000 INFO @ Sun, 03 Jun 2018 13:12:00: 13000000 INFO @ Sun, 03 Jun 2018 13:12:01: 13000000 INFO @ Sun, 03 Jun 2018 13:12:01: 13000000 INFO @ Sun, 03 Jun 2018 13:12:09: 14000000 INFO @ Sun, 03 Jun 2018 13:12:09: 14000000 INFO @ Sun, 03 Jun 2018 13:12:09: 14000000 INFO @ Sun, 03 Jun 2018 13:12:17: 15000000 INFO @ Sun, 03 Jun 2018 13:12:17: 15000000 INFO @ Sun, 03 Jun 2018 13:12:18: 15000000 INFO @ Sun, 03 Jun 2018 13:12:25: 16000000 INFO @ Sun, 03 Jun 2018 13:12:25: 16000000 INFO @ Sun, 03 Jun 2018 13:12:27: 16000000 INFO @ Sun, 03 Jun 2018 13:12:33: 17000000 INFO @ Sun, 03 Jun 2018 13:12:34: 17000000 INFO @ Sun, 03 Jun 2018 13:12:36: 17000000 INFO @ Sun, 03 Jun 2018 13:12:41: 18000000 INFO @ Sun, 03 Jun 2018 13:12:43: 18000000 INFO @ Sun, 03 Jun 2018 13:12:45: 18000000 INFO @ Sun, 03 Jun 2018 13:12:49: 19000000 INFO @ Sun, 03 Jun 2018 13:12:51: 19000000 INFO @ Sun, 03 Jun 2018 13:12:54: 19000000 INFO @ Sun, 03 Jun 2018 13:12:57: 20000000 INFO @ Sun, 03 Jun 2018 13:13:00: 20000000 INFO @ Sun, 03 Jun 2018 13:13:04: 20000000 INFO @ Sun, 03 Jun 2018 13:13:05: 21000000 INFO @ Sun, 03 Jun 2018 13:13:09: 21000000 INFO @ Sun, 03 Jun 2018 13:13:13: 21000000 INFO @ Sun, 03 Jun 2018 13:13:13: 22000000 INFO @ Sun, 03 Jun 2018 13:13:18: 22000000 INFO @ Sun, 03 Jun 2018 13:13:21: 23000000 INFO @ Sun, 03 Jun 2018 13:13:22: 22000000 INFO @ Sun, 03 Jun 2018 13:13:27: 23000000 INFO @ Sun, 03 Jun 2018 13:13:29: 24000000 INFO @ Sun, 03 Jun 2018 13:13:32: 23000000 INFO @ Sun, 03 Jun 2018 13:13:35: 24000000 INFO @ Sun, 03 Jun 2018 13:13:37: 25000000 INFO @ Sun, 03 Jun 2018 13:13:41: 24000000 INFO @ Sun, 03 Jun 2018 13:13:43: 25000000 INFO @ Sun, 03 Jun 2018 13:13:45: 26000000 INFO @ Sun, 03 Jun 2018 13:13:50: 25000000 INFO @ Sun, 03 Jun 2018 13:13:51: 26000000 INFO @ Sun, 03 Jun 2018 13:13:53: 27000000 INFO @ Sun, 03 Jun 2018 13:13:59: 26000000 INFO @ Sun, 03 Jun 2018 13:14:00: 27000000 INFO @ Sun, 03 Jun 2018 13:14:00: 28000000 INFO @ Sun, 03 Jun 2018 13:14:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:06: #1 total tags in treatment: 9353596 INFO @ Sun, 03 Jun 2018 13:14:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:06: #1 tags after filtering in treatment: 8062235 INFO @ Sun, 03 Jun 2018 13:14:06: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:14:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:07: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:14:07: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:07: #2 predicted fragment length is 81 bps INFO @ Sun, 03 Jun 2018 13:14:07: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 03 Jun 2018 13:14:07: #2.2 Generate R script for model : SRX4085378.20_model.r WARNING @ Sun, 03 Jun 2018 13:14:07: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:07: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 03 Jun 2018 13:14:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:08: 28000000 INFO @ Sun, 03 Jun 2018 13:14:08: 27000000 INFO @ Sun, 03 Jun 2018 13:14:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:13: #1 total tags in treatment: 9353596 INFO @ Sun, 03 Jun 2018 13:14:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:14: #1 tags after filtering in treatment: 8062235 INFO @ Sun, 03 Jun 2018 13:14:14: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:14:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:14: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:14:14: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:14: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:14: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:14: #2 predicted fragment length is 81 bps INFO @ Sun, 03 Jun 2018 13:14:14: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 03 Jun 2018 13:14:14: #2.2 Generate R script for model : SRX4085378.10_model.r WARNING @ Sun, 03 Jun 2018 13:14:14: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:14: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 03 Jun 2018 13:14:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:14: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:15: 28000000 INFO @ Sun, 03 Jun 2018 13:14:20: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:20: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:20: #1 total tags in treatment: 9353596 INFO @ Sun, 03 Jun 2018 13:14:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:20: #1 tags after filtering in treatment: 8062235 INFO @ Sun, 03 Jun 2018 13:14:20: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:14:20: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:20: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:14:20: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:20: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:21: #2 predicted fragment length is 81 bps INFO @ Sun, 03 Jun 2018 13:14:21: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 03 Jun 2018 13:14:21: #2.2 Generate R script for model : SRX4085378.05_model.r WARNING @ Sun, 03 Jun 2018 13:14:21: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:21: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 03 Jun 2018 13:14:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:25: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:35: #4 Write output xls file... SRX4085378.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:35: #4 Write peak in narrowPeak format file... SRX4085378.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:35: #4 Write summits bed file... SRX4085378.20_summits.bed INFO @ Sun, 03 Jun 2018 13:14:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1142 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:14:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:45: #4 Write output xls file... SRX4085378.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:45: #4 Write peak in narrowPeak format file... SRX4085378.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:45: #4 Write summits bed file... SRX4085378.10_summits.bed INFO @ Sun, 03 Jun 2018 13:14:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2452 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:14:48: #4 Write output xls file... SRX4085378.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:48: #4 Write peak in narrowPeak format file... SRX4085378.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:49: #4 Write summits bed file... SRX4085378.05_summits.bed INFO @ Sun, 03 Jun 2018 13:14:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4356 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。